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    ptprfa protein tyrosine phosphatase receptor type Fa [ Danio rerio (zebrafish) ]

    Gene ID: 140819, updated on 4-Jan-2025

    Summary

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    Official Symbol
    ptprfaprovided by ZNC
    Official Full Name
    protein tyrosine phosphatase receptor type Faprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-020107-2
    See related
    Ensembl:ENSDARG00000103479 AllianceGenome:ZFIN:ZDB-GENE-020107-2
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    LAR; ptprf
    Summary
    Predicted to enable protein tyrosine phosphatase activity. Acts upstream of or within sensory neuron axon guidance. Predicted to be located in plasma membrane. Is expressed in nervous system; pectoral fin; pharyngeal arch; and somite. Human ortholog(s) of this gene implicated in hyperinsulinism. Orthologous to human PTPRF (protein tyrosine phosphatase receptor type F). [provided by Alliance of Genome Resources, Jan 2025]
    Annotation information
    Annotation category: suggests misassembly
    Orthologs
    human mouse all
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    Genomic context

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    See ptprfa in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (2872279..3274488)
    105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (2595911..3112871)

    Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene KICSTOR complex protein SZT2 Neighboring gene hydroxypyruvate isomerase Neighboring gene uncharacterized LOC137495906 Neighboring gene lysine (K)-specific demethylase 4A, genome duplicate a Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 3a

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. LAR receptor tyrosine phosphatases and HSPGs guide peripheral sensory axons to the skin. Wang F, et al. Curr Biol, 2012 Mar 6. PMID 22326027, Free PMC Article
    2. Protein tyrosine phosphatase σ regulates the synapse number of zebrafish olfactory sensory neurons. Chen X, et al. J Neurochem, 2011 Nov. PMID 21812780
    3. Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. Hufton AL, et al. Genome Res, 2009 Nov. PMID 19704032, Free PMC Article
    4. Role of neurexin2a in lead-induced locomotor defect in developing zebrafish. Tu H, et al. Aquat Toxicol, 2018 Jan. PMID 29195096
    5. Differential oxidation of protein-tyrosine phosphatases during zebrafish caudal fin regeneration. Wu W, et al. Sci Rep, 2017 Aug 16. PMID 28814789, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoprotein phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein tyrosine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within protein dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within sensory neuron axon guidance IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within sensory neuron axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein tyrosine phosphatase receptor type Fa
    Names
    protein tyrosine phosphatase, receptor type, f, a
    zf-LAR
    NP_001298277.1
    XP_021332446.1
    XP_068077726.1
    XP_068077727.1
    XP_068077728.1
    XP_068077730.1
    XP_068077731.1
    XP_068077732.1
    XP_068077733.1
    XP_068077734.1
    XP_068077735.1
    XP_068077736.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001311348.1 → NP_001298277.1  protein tyrosine phosphatase receptor type Fa precursor

      Status: VALIDATED

      Source sequence(s)
      JQ414007
      UniProtKB/TrEMBL
      A0A8M9QA45, H9CWQ2
      Related
      ENSDARP00000150663.1, ENSDART00000181271.1
      Conserved Domains (9) summary
      cd00096
      Location:51 → 122
      Ig; Immunoglobulin domain
      cd05738
      Location:153 → 227
      Ig2_RPTP_IIa_LAR_like; Second immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR
      cd05739
      Location:247 → 315
      Ig3_RPTP_IIa_LAR_like; Third immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR
      smart00194
      Location:1339 → 1593
      PTPc; Protein tyrosine phosphatase, catalytic domain
      smart00410
      Location:142 → 226
      IG_like; Immunoglobulin like
      cd00047
      Location:1364 → 1593
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
      cd00063
      Location:320 → 409
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:34 → 125
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:609 → 696
      fn3; Fibronectin type III domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007117.7 Reference GRCz11 Primary Assembly

      Range
      2872279..3274488
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068221625.1 → XP_068077726.1  protein tyrosine phosphatase receptor type Fa isoform X1

      UniProtKB/TrEMBL
      A0A8M9PZE9, A0A8M9QA39

    2. XM_068221630.1 → XP_068077731.1  protein tyrosine phosphatase receptor type Fa isoform X5

      UniProtKB/TrEMBL
      A0A8M9PLU1, A0A8M9QA45

    3. XM_068221632.1 → XP_068077733.1  protein tyrosine phosphatase receptor type Fa isoform X7

      UniProtKB/TrEMBL
      A0A8M9PZF5

    4. XM_068221626.1 → XP_068077727.1  protein tyrosine phosphatase receptor type Fa isoform X2

      UniProtKB/TrEMBL
      A0A8M9PLT7
      Related
      ENSDARP00000138975.2, ENSDART00000171014.2

    5. XM_068221633.1 → XP_068077734.1  protein tyrosine phosphatase receptor type Fa isoform X8

      UniProtKB/TrEMBL
      A0A8M9PLU6, A0A8M9Q5Y4

    6. XM_068221627.1 → XP_068077728.1  protein tyrosine phosphatase receptor type Fa isoform X3

      UniProtKB/TrEMBL
      A0A8M9Q5Y1

    7. XM_068221629.1 → XP_068077730.1  protein tyrosine phosphatase receptor type Fa isoform X4

      UniProtKB/TrEMBL
      A0A8M9QF59

    8. XM_068221631.1 → XP_068077732.1  protein tyrosine phosphatase receptor type Fa isoform X6

      UniProtKB/TrEMBL
      A0A8M9QA45
      Related
      ENSDARP00000145445.1, ENSDART00000191485.1

    9. XM_068221634.1 → XP_068077735.1  protein tyrosine phosphatase receptor type Fa isoform X9

      UniProtKB/TrEMBL
      A0A8M9PZG0, A0A8M9QF62

    10. XM_068221635.1 → XP_068077736.1  protein tyrosine phosphatase receptor type Fa isoform X10

      UniProtKB/TrEMBL
      A0A8M9QA48, A0A8M9QF62

    11. XM_021476771.2 → XP_021332446.1  protein tyrosine phosphatase receptor type Fa isoform X10

      UniProtKB/TrEMBL
      A0A8M9QA48, A0A8M9QF62
      Related
      ENSDARP00000155993.1, ENSDART00000183181.1
      Conserved Domains (5) summary
      cd05739
      Location:246 → 314
      Ig3_RPTP_IIa_LAR_like; Third immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR
      cd00047
      Location:1261 → 1490
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
      cd00063
      Location:319 → 408
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:33 → 124
      I-set; Immunoglobulin I-set domain
      cd05738
      Location:152 → 226
      Ig2_RPTP_IIa_LAR_like; Second immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR
    Nucleotide Protein Strain
    Heading Accession and Version

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